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Answers to frequently asked questions about datasets generated in the Balasubramanian group
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README.md

README.md


Observed DNA G-quadruplex sequences in the human genome

The DNA G-quadruplex annotation of the human genome as presented in Chambers et al., 2015 is available in GEO GSE63874 - see Supplementary files.

The files to use are the observed G-quadruplex sequences in common to the 2 K+ experiments as detected on the forward and reverse strands respectively with coordinates from the human hg19 reference genome:

  • GSE63874_Na_K_minus_hits_intersect.bed.gz
  • GSE63874_Na_K_plus_hits_intersect.bed.gz

The formatting of these files is:

  • 1st column: chromosome
  • 2nd column: start of the observed G-quadruplex
  • 3rd column: end of the observed G-quadruplex

You can use bedtools if you'd like to merge the two files above using the following command:

bedtools merge -i <(zcat GSE63874_Na_K_* | bedtools sort -i) > GSE63874_Na_K.bed

These files and others are publicly available to download from GEO in the following link:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63874

for more details about each individual file type and design, please read this:

ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63874/suppl/GSE63874%5FREADME%2Etxt

A more recently updated map of observed G-quadruplex sequences in the human genome is available in GEO GSE110582. Go to the Samples section and select Homo_Li_K GSM3003539. The files to use are the correspond to the K+ experiments as detected on the forward and reverse strands respectively with coordinates from the human hg19 reference genome:

  • GSM3003539_Homo_all_w15_th-1_minus.hits.max.K.w50.25.bed.gz
  • GSM3003539_Homo_all_w15_th-1_plus.hits.max.K.w50.25.bed.gz

The formatting of these files is:

  • 1st column: chromosome
  • 2nd column: start of the observed G-quadruplex
  • 3rd column: end of the observed G-quadruplex
  • 4th column: score

Observed DNA G-quadruplex sequences in multiple species

The DNA G-quadruplex annotation in multiple species as presented in Marsico et al., 2019 is available in GEO GSE110582.

Go to the Samples section and find your species of interest and the condition used in the experiment, e.g. Homo sampiens and K+ experiment Homo_Li_K GSM3003539. The files to use are *.hits.max.K.w50.25.bed.gz. The formatting of these files is:

  • 1st column: chromosome
  • 2nd column: start of the observed G-quadruplex
  • 3rd column: end of the observed G-quadruplex
  • 4th column: score

Observed RNA G-quadruplex sequences in the human transcriptome

The RNA G-quadruplex annotation of the human transcriptome as presented in Kwok et al., 2016 is available in GEO GSE77282.

Scroll down to the Supplementary files section. The file to use is GSE77282_K_hits.bed.gz.

Genome-wide mapping of 5hmU and base J in Leishmania

The 5hmU maps in the Leishmania donovani and Leishmania major genomes as presented in Kawasaki et al., 2017 are available in GEO GSE83384.

Go to the Samples section and find your species of interest (Lmaj - major, Ldon - donovani) and the methodology used to map 5hmU (DIP, chem) or J, e.g. L. major chmemical enrichment rep 1 fk050_Lmaj_chem1 GSM2200481. The file to use ends with *.peaks.txt.gz.

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